Starting phenix.real_space_refine on Sat Jul 26 12:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eit_28164/07_2025/8eit_28164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eit_28164/07_2025/8eit_28164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eit_28164/07_2025/8eit_28164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eit_28164/07_2025/8eit_28164.map" model { file = "/net/cci-nas-00/data/ceres_data/8eit_28164/07_2025/8eit_28164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eit_28164/07_2025/8eit_28164.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5453 2.51 5 N 1480 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8578 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1821 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2565 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 422 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1961 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HXA:plan-3': 1, 'HXA:plan-5': 1, 'HXA:plan-4': 1, 'HXA:plan-7': 1, 'HXA:plan-6': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 6.41, per 1000 atoms: 0.75 Number of scatterers: 8578 At special positions: 0 Unit cell: (100.44, 119.88, 125.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1596 8.00 N 1480 7.00 C 5453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.111A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 4.403A pdb=" N TRP A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 89' Processing helix chain 'A' and resid 90 through 93 removed outlier: 3.829A pdb=" N ASN A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.687A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 235 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.534A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 26 Processing helix chain 'C' and resid 29 through 42 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.209A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.564A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.569A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.030A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 4.000A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG R 37 " --> pdb=" O HIS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 68 Proline residue: R 60 - end of helix removed outlier: 3.585A pdb=" N ALA R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.534A pdb=" N PHE R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 107 removed outlier: 5.270A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 117 Processing helix chain 'R' and resid 119 through 143 removed outlier: 3.511A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 Proline residue: R 181 - end of helix Processing helix chain 'R' and resid 191 through 212 Processing helix chain 'R' and resid 215 through 226 Processing helix chain 'R' and resid 226 through 236 removed outlier: 4.667A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.192A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 4.686A pdb=" N VAL A 78 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 97 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.266A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.908A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.024A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.565A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.382A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.668A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.737A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.000A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 4.182A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL E 149 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 160 through 161 removed outlier: 3.586A pdb=" N VAL R 169 " --> pdb=" O ASN R 161 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2792 1.34 - 1.46: 2064 1.46 - 1.58: 3843 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8765 Sorted by residual: bond pdb=" C4 HXA R 401 " pdb=" C5 HXA R 401 " ideal model delta sigma weight residual 1.332 1.531 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 HXA R 401 " pdb=" C4 HXA R 401 " ideal model delta sigma weight residual 1.496 1.530 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C5 HXA R 401 " pdb=" C6 HXA R 401 " ideal model delta sigma weight residual 1.503 1.529 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C6 HXA R 401 " pdb=" C7 HXA R 401 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" CG1 ILE R 130 " pdb=" CD1 ILE R 130 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 ... (remaining 8760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 11762 2.57 - 5.15: 117 5.15 - 7.72: 22 7.72 - 10.30: 3 10.30 - 12.87: 2 Bond angle restraints: 11906 Sorted by residual: angle pdb=" C3 HXA R 401 " pdb=" C4 HXA R 401 " pdb=" C5 HXA R 401 " ideal model delta sigma weight residual 128.39 115.52 12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C4 HXA R 401 " pdb=" C5 HXA R 401 " pdb=" C6 HXA R 401 " ideal model delta sigma weight residual 127.44 115.45 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N ASP C 48 " pdb=" CA ASP C 48 " pdb=" C ASP C 48 " ideal model delta sigma weight residual 109.64 114.51 -4.87 1.27e+00 6.20e-01 1.47e+01 angle pdb=" N ARG C 13 " pdb=" CA ARG C 13 " pdb=" CB ARG C 13 " ideal model delta sigma weight residual 110.12 115.34 -5.22 1.47e+00 4.63e-01 1.26e+01 angle pdb=" C ALA C 10 " pdb=" N GLN C 11 " pdb=" CA GLN C 11 " ideal model delta sigma weight residual 121.18 114.98 6.20 1.98e+00 2.55e-01 9.82e+00 ... (remaining 11901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 4659 16.83 - 33.67: 400 33.67 - 50.50: 77 50.50 - 67.33: 9 67.33 - 84.17: 10 Dihedral angle restraints: 5155 sinusoidal: 1932 harmonic: 3223 Sorted by residual: dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA LEU R 59 " pdb=" C LEU R 59 " pdb=" N PRO R 60 " pdb=" CA PRO R 60 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE R 82 " pdb=" C PHE R 82 " pdb=" N ALA R 83 " pdb=" CA ALA R 83 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1043 0.050 - 0.100: 235 0.100 - 0.150: 62 0.150 - 0.200: 6 0.200 - 0.250: 3 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CB THR A 169 " pdb=" CA THR A 169 " pdb=" OG1 THR A 169 " pdb=" CG2 THR A 169 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE C 9 " pdb=" CA ILE C 9 " pdb=" CG1 ILE C 9 " pdb=" CG2 ILE C 9 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1346 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PRO E 75 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO C 49 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 238 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO R 239 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " -0.032 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1358 2.76 - 3.30: 7951 3.30 - 3.83: 14467 3.83 - 4.37: 16781 4.37 - 4.90: 29308 Nonbonded interactions: 69865 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.230 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR R 240 " pdb=" O1 HXA R 401 " model vdw 2.292 3.040 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.311 3.040 nonbonded pdb=" OG SER R 268 " pdb=" OD1 ASN R 272 " model vdw 2.319 3.040 ... (remaining 69860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 28.840 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:48.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 8766 Z= 0.177 Angle : 0.685 12.870 11908 Z= 0.351 Chirality : 0.047 0.250 1349 Planarity : 0.005 0.063 1523 Dihedral : 13.351 84.169 3080 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1101 helix: 1.64 (0.26), residues: 370 sheet: 1.01 (0.32), residues: 250 loop : -0.03 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.009 0.001 HIS R 86 PHE 0.021 0.002 PHE R 82 TYR 0.024 0.001 TYR E 190 ARG 0.015 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.12451 ( 450) hydrogen bonds : angle 5.82093 ( 1284) SS BOND : bond 0.00513 ( 1) SS BOND : angle 1.10121 ( 2) covalent geometry : bond 0.00355 ( 8765) covalent geometry : angle 0.68458 (11906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 1.186 Fit side-chains REVERT: R 137 HIS cc_start: 0.7464 (m-70) cc_final: 0.6614 (m-70) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 1.2826 time to fit residues: 256.7713 Evaluate side-chains 143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 215 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN B 155 ASN R 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099054 restraints weight = 13408.970| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.51 r_work: 0.3162 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8766 Z= 0.169 Angle : 0.598 10.017 11908 Z= 0.309 Chirality : 0.044 0.281 1349 Planarity : 0.005 0.067 1523 Dihedral : 5.347 77.698 1220 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.00 % Allowed : 13.41 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1101 helix: 2.24 (0.27), residues: 384 sheet: 0.90 (0.32), residues: 262 loop : 0.07 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE B 234 TYR 0.022 0.002 TYR E 190 ARG 0.007 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 450) hydrogen bonds : angle 4.57394 ( 1284) SS BOND : bond 0.00872 ( 1) SS BOND : angle 2.73892 ( 2) covalent geometry : bond 0.00386 ( 8765) covalent geometry : angle 0.59740 (11906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.934 Fit side-chains REVERT: B 254 ASP cc_start: 0.8761 (t0) cc_final: 0.8534 (t0) REVERT: C 32 LYS cc_start: 0.8774 (tppt) cc_final: 0.8097 (tppt) REVERT: E 87 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7154 (mmt90) REVERT: E 223 ASP cc_start: 0.7374 (m-30) cc_final: 0.6880 (m-30) REVERT: R 6 GLN cc_start: 0.8204 (mp10) cc_final: 0.7854 (mt0) REVERT: R 52 ASP cc_start: 0.8047 (t70) cc_final: 0.7806 (t70) REVERT: R 137 HIS cc_start: 0.7606 (m-70) cc_final: 0.6788 (m-70) REVERT: R 188 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8883 (mp) REVERT: R 259 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8661 (mtpp) outliers start: 18 outliers final: 8 residues processed: 170 average time/residue: 1.1602 time to fit residues: 210.0679 Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN R 23 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.098853 restraints weight = 13453.794| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.54 r_work: 0.3160 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8766 Z= 0.136 Angle : 0.554 7.004 11908 Z= 0.289 Chirality : 0.043 0.184 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.649 56.811 1218 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.44 % Allowed : 16.74 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1101 helix: 2.35 (0.27), residues: 385 sheet: 0.93 (0.32), residues: 260 loop : 0.07 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.021 0.001 TYR E 190 ARG 0.008 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 450) hydrogen bonds : angle 4.36687 ( 1284) SS BOND : bond 0.00465 ( 1) SS BOND : angle 1.32932 ( 2) covalent geometry : bond 0.00307 ( 8765) covalent geometry : angle 0.55340 (11906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.944 Fit side-chains REVERT: C 19 LEU cc_start: 0.6688 (tp) cc_final: 0.6483 (tp) REVERT: C 32 LYS cc_start: 0.8600 (tppt) cc_final: 0.8226 (tppt) REVERT: E 87 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7129 (mmt90) REVERT: E 220 GLU cc_start: 0.7198 (mp0) cc_final: 0.6983 (mp0) REVERT: E 223 ASP cc_start: 0.7360 (m-30) cc_final: 0.6848 (m-30) REVERT: R 23 ASN cc_start: 0.8407 (m-40) cc_final: 0.7962 (m110) REVERT: R 137 HIS cc_start: 0.7590 (m-70) cc_final: 0.6761 (m-70) REVERT: R 188 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8902 (mp) REVERT: R 218 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7836 (mtt90) REVERT: R 259 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8652 (mtpp) outliers start: 22 outliers final: 9 residues processed: 165 average time/residue: 1.1619 time to fit residues: 204.6010 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097720 restraints weight = 13360.065| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.51 r_work: 0.3141 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8766 Z= 0.150 Angle : 0.554 7.255 11908 Z= 0.290 Chirality : 0.043 0.168 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.631 56.681 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.99 % Allowed : 17.18 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.26), residues: 1101 helix: 2.47 (0.27), residues: 379 sheet: 0.88 (0.31), residues: 269 loop : 0.14 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.024 0.002 PHE R 200 TYR 0.021 0.001 TYR E 190 ARG 0.011 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 450) hydrogen bonds : angle 4.31070 ( 1284) SS BOND : bond 0.00514 ( 1) SS BOND : angle 1.33403 ( 2) covalent geometry : bond 0.00343 ( 8765) covalent geometry : angle 0.55355 (11906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.927 Fit side-chains REVERT: B 228 ASP cc_start: 0.8745 (m-30) cc_final: 0.8494 (m-30) REVERT: C 19 LEU cc_start: 0.6704 (tp) cc_final: 0.6494 (tp) REVERT: C 32 LYS cc_start: 0.8442 (tppt) cc_final: 0.8141 (tppt) REVERT: E 87 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7149 (mmt90) REVERT: R 6 GLN cc_start: 0.8294 (mp10) cc_final: 0.8047 (mt0) REVERT: R 23 ASN cc_start: 0.8356 (m-40) cc_final: 0.8004 (m110) REVERT: R 52 ASP cc_start: 0.8005 (t70) cc_final: 0.7796 (t70) REVERT: R 135 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8173 (mm) REVERT: R 137 HIS cc_start: 0.7610 (m-70) cc_final: 0.6812 (m-70) REVERT: R 188 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8871 (mp) REVERT: R 218 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7866 (mtt90) REVERT: R 259 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8691 (mtpp) outliers start: 27 outliers final: 12 residues processed: 166 average time/residue: 1.2428 time to fit residues: 219.4500 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097326 restraints weight = 13239.379| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.47 r_work: 0.3135 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8766 Z= 0.152 Angle : 0.556 7.498 11908 Z= 0.292 Chirality : 0.043 0.163 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.607 54.143 1218 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.44 % Allowed : 17.85 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1101 helix: 2.50 (0.27), residues: 379 sheet: 0.89 (0.31), residues: 268 loop : 0.15 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE R 200 TYR 0.022 0.001 TYR E 190 ARG 0.011 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 450) hydrogen bonds : angle 4.29309 ( 1284) SS BOND : bond 0.00469 ( 1) SS BOND : angle 1.03102 ( 2) covalent geometry : bond 0.00348 ( 8765) covalent geometry : angle 0.55600 (11906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.042 Fit side-chains REVERT: A 70 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8323 (mmmt) REVERT: C 19 LEU cc_start: 0.6693 (tp) cc_final: 0.6465 (tp) REVERT: C 32 LYS cc_start: 0.8445 (tppt) cc_final: 0.8166 (tppt) REVERT: E 87 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7181 (mmt90) REVERT: E 219 LEU cc_start: 0.8270 (mp) cc_final: 0.7602 (tt) REVERT: R 53 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8532 (tp) REVERT: R 135 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8163 (mm) REVERT: R 137 HIS cc_start: 0.7745 (m-70) cc_final: 0.6906 (m-70) REVERT: R 188 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8868 (mp) REVERT: R 218 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (mtt90) REVERT: R 259 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8703 (mtpp) outliers start: 31 outliers final: 15 residues processed: 166 average time/residue: 1.1790 time to fit residues: 208.1729 Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 0.0770 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098481 restraints weight = 13189.277| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.50 r_work: 0.3156 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8766 Z= 0.123 Angle : 0.550 7.667 11908 Z= 0.286 Chirality : 0.043 0.224 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.424 52.066 1218 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.22 % Allowed : 19.07 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.26), residues: 1101 helix: 2.59 (0.27), residues: 378 sheet: 1.00 (0.32), residues: 258 loop : 0.16 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.013 0.001 PHE R 200 TYR 0.020 0.001 TYR E 190 ARG 0.012 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 450) hydrogen bonds : angle 4.19072 ( 1284) SS BOND : bond 0.00401 ( 1) SS BOND : angle 0.73552 ( 2) covalent geometry : bond 0.00277 ( 8765) covalent geometry : angle 0.54992 (11906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.014 Fit side-chains REVERT: A 70 LYS cc_start: 0.8531 (mmtm) cc_final: 0.8310 (mmmt) REVERT: C 19 LEU cc_start: 0.6684 (tp) cc_final: 0.6443 (tp) REVERT: C 32 LYS cc_start: 0.8506 (tppt) cc_final: 0.8287 (tppt) REVERT: E 46 GLU cc_start: 0.8509 (tt0) cc_final: 0.8264 (pt0) REVERT: E 87 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7147 (mmt90) REVERT: E 219 LEU cc_start: 0.8297 (mp) cc_final: 0.7593 (tt) REVERT: R 6 GLN cc_start: 0.8438 (mp10) cc_final: 0.8173 (mt0) REVERT: R 53 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8507 (tp) REVERT: R 135 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8061 (mm) REVERT: R 137 HIS cc_start: 0.7712 (m-70) cc_final: 0.6859 (m-70) REVERT: R 188 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8867 (mp) REVERT: R 259 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8687 (mtpp) outliers start: 29 outliers final: 14 residues processed: 168 average time/residue: 1.2107 time to fit residues: 216.3410 Evaluate side-chains 161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099036 restraints weight = 13362.542| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.50 r_work: 0.3164 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8766 Z= 0.119 Angle : 0.561 7.894 11908 Z= 0.289 Chirality : 0.042 0.192 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.320 49.111 1218 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.33 % Allowed : 19.84 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1101 helix: 2.57 (0.27), residues: 378 sheet: 1.06 (0.31), residues: 257 loop : 0.16 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.018 0.001 TYR E 190 ARG 0.012 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 450) hydrogen bonds : angle 4.15077 ( 1284) SS BOND : bond 0.00330 ( 1) SS BOND : angle 0.66738 ( 2) covalent geometry : bond 0.00268 ( 8765) covalent geometry : angle 0.56122 (11906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.931 Fit side-chains REVERT: C 19 LEU cc_start: 0.6613 (tp) cc_final: 0.6410 (tp) REVERT: E 46 GLU cc_start: 0.8478 (tt0) cc_final: 0.8247 (pt0) REVERT: E 87 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7143 (mmt90) REVERT: R 6 GLN cc_start: 0.8381 (mp10) cc_final: 0.8157 (mt0) REVERT: R 53 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8651 (tp) REVERT: R 135 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8073 (mm) REVERT: R 137 HIS cc_start: 0.7703 (m-70) cc_final: 0.6851 (m-70) REVERT: R 188 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8865 (mp) REVERT: R 202 TYR cc_start: 0.9345 (t80) cc_final: 0.9141 (t80) REVERT: R 259 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8685 (mtpp) outliers start: 30 outliers final: 16 residues processed: 173 average time/residue: 1.2277 time to fit residues: 226.2709 Evaluate side-chains 163 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099798 restraints weight = 13402.343| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.50 r_work: 0.3179 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8766 Z= 0.113 Angle : 0.572 8.943 11908 Z= 0.294 Chirality : 0.042 0.163 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.217 44.602 1218 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.99 % Allowed : 20.73 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.26), residues: 1101 helix: 2.61 (0.27), residues: 378 sheet: 1.06 (0.31), residues: 257 loop : 0.18 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 253 TYR 0.016 0.001 TYR E 190 ARG 0.012 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 450) hydrogen bonds : angle 4.14894 ( 1284) SS BOND : bond 0.00363 ( 1) SS BOND : angle 0.51319 ( 2) covalent geometry : bond 0.00254 ( 8765) covalent geometry : angle 0.57224 (11906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.941 Fit side-chains REVERT: A 222 ASP cc_start: 0.8728 (m-30) cc_final: 0.8499 (m-30) REVERT: B 123 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9099 (mt) REVERT: C 19 LEU cc_start: 0.6584 (tp) cc_final: 0.6378 (tp) REVERT: E 46 GLU cc_start: 0.8450 (tt0) cc_final: 0.8239 (pt0) REVERT: R 135 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8041 (mm) REVERT: R 137 HIS cc_start: 0.7682 (m-70) cc_final: 0.6787 (m-70) REVERT: R 188 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8867 (mp) REVERT: R 211 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7759 (mtt90) REVERT: R 259 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8684 (mtpp) outliers start: 27 outliers final: 13 residues processed: 168 average time/residue: 1.1567 time to fit residues: 207.1975 Evaluate side-chains 162 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 211 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.134758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099727 restraints weight = 13319.243| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.50 r_work: 0.3179 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8766 Z= 0.121 Angle : 0.591 8.112 11908 Z= 0.305 Chirality : 0.042 0.155 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.200 40.334 1218 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.55 % Allowed : 21.51 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.26), residues: 1101 helix: 2.56 (0.27), residues: 378 sheet: 1.09 (0.31), residues: 257 loop : 0.20 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.017 0.001 TYR E 190 ARG 0.015 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 450) hydrogen bonds : angle 4.17366 ( 1284) SS BOND : bond 0.00399 ( 1) SS BOND : angle 0.56871 ( 2) covalent geometry : bond 0.00276 ( 8765) covalent geometry : angle 0.59111 (11906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8729 (m-30) cc_final: 0.8506 (m-30) REVERT: B 123 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9103 (mt) REVERT: C 19 LEU cc_start: 0.6587 (tp) cc_final: 0.6379 (tp) REVERT: E 46 GLU cc_start: 0.8437 (tt0) cc_final: 0.8204 (pt0) REVERT: R 6 GLN cc_start: 0.8554 (mp10) cc_final: 0.8123 (mt0) REVERT: R 135 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8053 (mm) REVERT: R 137 HIS cc_start: 0.7693 (m-70) cc_final: 0.6808 (m-70) REVERT: R 188 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8876 (mp) REVERT: R 211 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7754 (mtt90) REVERT: R 259 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8688 (mtpp) outliers start: 23 outliers final: 14 residues processed: 163 average time/residue: 1.1466 time to fit residues: 199.5479 Evaluate side-chains 162 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 211 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099371 restraints weight = 13351.076| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.50 r_work: 0.3171 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8766 Z= 0.126 Angle : 0.608 8.878 11908 Z= 0.311 Chirality : 0.043 0.153 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.219 35.756 1218 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.33 % Allowed : 22.28 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1101 helix: 2.52 (0.27), residues: 378 sheet: 1.04 (0.32), residues: 259 loop : 0.23 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 450) hydrogen bonds : angle 4.20522 ( 1284) SS BOND : bond 0.00442 ( 1) SS BOND : angle 0.57876 ( 2) covalent geometry : bond 0.00288 ( 8765) covalent geometry : angle 0.60795 (11906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.940 Fit side-chains REVERT: B 123 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9076 (mt) REVERT: C 19 LEU cc_start: 0.6597 (tp) cc_final: 0.6388 (tp) REVERT: R 6 GLN cc_start: 0.8537 (mp10) cc_final: 0.8157 (mt0) REVERT: R 135 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8044 (mm) REVERT: R 137 HIS cc_start: 0.7662 (m-70) cc_final: 0.6798 (m-70) REVERT: R 188 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8892 (mp) outliers start: 21 outliers final: 14 residues processed: 163 average time/residue: 1.1476 time to fit residues: 199.7985 Evaluate side-chains 162 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 82 GLN R 244 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093041 restraints weight = 13445.454| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.54 r_work: 0.3062 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8766 Z= 0.296 Angle : 0.743 12.096 11908 Z= 0.384 Chirality : 0.048 0.212 1349 Planarity : 0.005 0.059 1523 Dihedral : 5.261 56.782 1218 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 22.39 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1101 helix: 2.20 (0.27), residues: 378 sheet: 0.83 (0.31), residues: 272 loop : 0.13 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 131 HIS 0.007 0.002 HIS E 35 PHE 0.018 0.002 PHE B 180 TYR 0.028 0.002 TYR E 190 ARG 0.019 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 450) hydrogen bonds : angle 4.61948 ( 1284) SS BOND : bond 0.00663 ( 1) SS BOND : angle 1.12528 ( 2) covalent geometry : bond 0.00687 ( 8765) covalent geometry : angle 0.74251 (11906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8476.36 seconds wall clock time: 144 minutes 52.18 seconds (8692.18 seconds total)